[uktokyoite]

I agree with Godwine - Kansai has all of these things if you don't want to spend all your time traveling. Unfortunately, I haven't been to Kyushu either so I have no idea about that area.

If you like the mountains and nature they you should try going to the Mount Takao area to the NE of Tokyo. Takao is usually pretty busy as it is now well established on the tourist trail both for Japanese and non-Japanese but it is surrounded by other mountains that are equally beautiful.